%  Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
%  The output image format and file extension will be the same as the
%  input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
%  extension that you specified will be ignored.
%
%  Usage: save_untouch_nii(nii, filename)
%  
%  nii - nii structure that is loaded by "load_untouch_nii.m"
%
%  filename  - 	NIFTI or ANALYZE file name.
%
%  - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function save_untouch_nii(nii, filename)
   
   if ~exist('nii','var') | isempty(nii) | ~isfield(nii,'hdr') | ...
	~isfield(nii,'img') | ~exist('filename','var') | isempty(filename)

      error('Usage: save_untouch_nii(nii, filename)');
   end

   if ~isfield(nii,'untouch') | nii.untouch == 0
      error('Usage: please use ''save_nii.m'' for the modified structure.');
   end

   if isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'ni1')
      filetype = 1;
   elseif isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'n+1')
      filetype = 2;
   else
      filetype = 0;
   end

   v = version;

   %  Check file extension. If .gz, unpack it into temp folder
   %
   if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')

      if ~strcmp(filename(end-6:end), '.img.gz') & ...
	 ~strcmp(filename(end-6:end), '.hdr.gz') & ...
	 ~strcmp(filename(end-6:end), '.nii.gz')

         error('Please check filename.');
      end

      if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
         error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
      else
         gzFile = 1;
         filename = filename(1:end-3);
      end
   end

   [p,f] = fileparts(filename);
   fileprefix = fullfile(p, f);

   write_nii(nii, filetype, fileprefix);

   %  gzip output file if requested
   %
   if exist('gzFile', 'var')
      if filetype == 1
         gzip([fileprefix, '.img']);
         delete([fileprefix, '.img']);
         gzip([fileprefix, '.hdr']);
         delete([fileprefix, '.hdr']);
      elseif filetype == 2
         gzip([fileprefix, '.nii']);
         delete([fileprefix, '.nii']);
      end;
   end;

%   %  So earlier versions of SPM can also open it with correct originator
 %  %
  % if filetype == 0
   %   M=[[diag(nii.hdr.dime.pixdim(2:4)) -[nii.hdr.hist.originator(1:3).*nii.hdr.dime.pixdim(2:4)]'];[0 0 0 1]];
    %  save(fileprefix, 'M');
%   elseif filetype == 1
 %     M=[];
  %    save(fileprefix, 'M');
   %end
   
   return					% save_untouch_nii


%-----------------------------------------------------------------------------------
function write_nii(nii, filetype, fileprefix)

   hdr = nii.hdr;

   if isfield(nii,'ext') & ~isempty(nii.ext)
      ext = nii.ext;
      [ext, esize_total] = verify_nii_ext(ext);
   else
      ext = [];
   end

   switch double(hdr.dime.datatype),
   case   1,
      hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
   case   2,
      hdr.dime.bitpix = int16(8 ); precision = 'uint8';
   case   4,
      hdr.dime.bitpix = int16(16); precision = 'int16';
   case   8,
      hdr.dime.bitpix = int16(32); precision = 'int32';
   case  16,
      hdr.dime.bitpix = int16(32); precision = 'float32';
   case  32,
      hdr.dime.bitpix = int16(64); precision = 'float32';
   case  64,
      hdr.dime.bitpix = int16(64); precision = 'float64';
   case 128,
      hdr.dime.bitpix = int16(24); precision = 'uint8';
   case 256 
      hdr.dime.bitpix = int16(8 ); precision = 'int8';
   case 512 
      hdr.dime.bitpix = int16(16); precision = 'uint16';
   case 768 
      hdr.dime.bitpix = int16(32); precision = 'uint32';
   case 1024
      hdr.dime.bitpix = int16(64); precision = 'int64';
   case 1280
      hdr.dime.bitpix = int16(64); precision = 'uint64';
   case 1792,
      hdr.dime.bitpix = int16(128); precision = 'float64';
   otherwise
      error('This datatype is not supported');
   end
   
%   hdr.dime.glmax = round(double(max(nii.img(:))));
 %  hdr.dime.glmin = round(double(min(nii.img(:))));
   
   if filetype == 2
      fid = fopen(sprintf('%s.nii',fileprefix),'w');
      
      if fid < 0,
         msg = sprintf('Cannot open file %s.nii.',fileprefix);
         error(msg);
      end
      
      hdr.dime.vox_offset = 352;

      if ~isempty(ext)
         hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
      end

      hdr.hist.magic = 'n+1';
      save_untouch_nii_hdr(hdr, fid);

      if ~isempty(ext)
         save_nii_ext(ext, fid);
      end
   elseif filetype == 1
      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
      
      if fid < 0,
         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
         error(msg);
      end
      
      hdr.dime.vox_offset = 0;
      hdr.hist.magic = 'ni1';
      save_untouch_nii_hdr(hdr, fid);

      if ~isempty(ext)
         save_nii_ext(ext, fid);
      end
      
      fclose(fid);
      fid = fopen(sprintf('%s.img',fileprefix),'w');
   else
      fid = fopen(sprintf('%s.hdr',fileprefix),'w');
      
      if fid < 0,
         msg = sprintf('Cannot open file %s.hdr.',fileprefix);
         error(msg);
      end
      
      save_untouch0_nii_hdr(hdr, fid);
      
      fclose(fid);
      fid = fopen(sprintf('%s.img',fileprefix),'w');
   end

   ScanDim = double(hdr.dime.dim(5));		% t
   SliceDim = double(hdr.dime.dim(4));		% z
   RowDim   = double(hdr.dime.dim(3));		% y
   PixelDim = double(hdr.dime.dim(2));		% x
   SliceSz  = double(hdr.dime.pixdim(4));
   RowSz    = double(hdr.dime.pixdim(3));
   PixelSz  = double(hdr.dime.pixdim(2));
   
   x = 1:PixelDim;
   
   if filetype == 2 & isempty(ext)
      skip_bytes = double(hdr.dime.vox_offset) - 348;
   else
      skip_bytes = 0;
   end

   if double(hdr.dime.datatype) == 128

      %  RGB planes are expected to be in the 4th dimension of nii.img
      %
      if(size(nii.img,4)~=3)
         error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
      end

      nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
   end

   %  For complex float32 or complex float64, voxel values
   %  include [real, imag]
   %
   if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
      real_img = real(nii.img(:))';
      nii.img = imag(nii.img(:))';
      nii.img = [real_img; nii.img];
   end

   if skip_bytes
      fwrite(fid, zeros(1,skip_bytes), 'uint8');
   end

   fwrite(fid, nii.img, precision);
%   fwrite(fid, nii.img, precision, skip_bytes);        % error using skip
   fclose(fid);

   return;					% write_nii

